At birth, an infant's immune system is extremely tolerant of everything, which is why infants are more vulnerable to infection. Slowly over the first couple years of life, the immune system matures. This process is complex, and it involves learning about which microorganisms are acceptable and can be ignored and which are harmful and should be killed. The microbes in and on the body help to train the immature immune system in a process that is not yet completely understood but ends with proper responses by the mature immune system.
Many different illnesses — including type 1 diabetes, celiac disease, asthma, Crohn's disease, and ulcerative colitis — are thought to have complex causes stemming partially from a genetic predisposition and partially from an environmental stimulus. A loss of some beneficial microbes from the human microbiota (the community of microorganisms that live in and on us) could also be contributing to the development of these conditions in increasing numbers of people.
What's causing these microbes to disappear? Possibly overuse of antibiotics, as well as the widespread use of antibiotics given to livestock that end up in our systems. The increased use of caesarean section instead of vaginal delivery may also interfere with inoculation of an infant with the mother's microbes.
What's the impact of this loss of a healthy microbiota? Consider the case of one bacteria in particular, Helicobacter pylori. Over 30 years ago, H. pylori was found in one out of every four adults, colonizing the lining of the stomach. It was causing people to become very ill with gastritis and peptic ulcers that could turn into stomach cancer. H. pylori was degrading the mucosa of the stomach and allowing gastric juices to destroy the lining even more. The treatment for these conditions was to get rid of an H. pylori infection with antibiotics, a strategy that effectively reduced its presence in most developed countries. In the years since, high rates of ulcers and H. pylori have decreased, but rates of esophageal cancer have increased. This has led H. pylori expert Dr. Martin Blaser to look into the link between the loss of this bacteria that was not causing harm in most people and esophageal reflux and cancer. It's unclear how loss of a pathogenic microbe can contribute to another human disease, but it appears that over the long course of our co-evolution with this bacterium, we may have come to need each other.
What does this mean for you? As we learn about microorganisms, we find they may be causing disease in some people, but this does not necessarily mean they're harmful in all people. By eliminating harmless bacteria, we're shifting the community of microorganisms in ways that we don't yet fully understand. Understanding how microorganisms work together in their communities, especially when associated with humans, is still a very young science with a lot of progress yet to be made before we know all the downstream consequences of many treatments against microbes.